Full Genome Sequencing

From Biouniverse.net

Full genome sequencing (FGS), also known as whole genome sequencing, complete genome sequencing, or entire genome sequencing, is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time.

This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria or chloroplast, depending respectively on whether the organism is an animal or plant. Almost any biological sample—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, hair (as long as the hair contains a hair follicle), seeds, plant leaves, or anything else that has DNA-containing cells. Because the sequence data that is produced can be quite large (for example, there are approximately six billion base pairs in each human diploid genome), genomic data is stored electronically and requires a large amount of computing power and storage capacity. Full genome sequencing would have been nearly impossible before the advent of the microprocessor, computers, and the Information Age.

Full genome sequencing should thus not be confused with DNA profiling. The latter only determines the likelihood that genetic material came from a particular individual or group and does not contain additional information on genetic relationships, origin or suspectability on specific diseases. [1]. It is also distinct from SNP genotyping which covers less than 0.1% of the genome. Almost all truly complete genomes are of microbes, the term "full genome" is sometimes used loosely to mean "greater than 95%". The remainder of this article focuses on nearly complete human genomes.

Full genome sequencing only refers to the laboratory process of deducing a person's entire genetic code and, on its own, may not contain any clinical assessment or useful clinical information. However, this may change over time as a large number of scientific studies continue to be published detailing clear associations between specific genetic variants and disease.[2][3]

The first nearly complete human genomes sequenced were J. Craig Venter's (caucasian male at 7.5-fold average coverage) [4][5][6] and James Watson's (caucasian male at 7.4-fold).[7][8][9], a Han Chinese (YH at 36-fold) [10], a Yoruban from Nigeria (at 30-fold) [11], a female leukemia patient (at 33 and 14-fold coverage for tumor and normal tissues)[12], and Seong-Jin Kim (Korean at 29-fold) [13]. Other full genomes have been sequenced but not published, and as of June 2009, commercialization of full genome sequencing is in an early stage and growing rapidly.

New techniques

One possible way to accomplish the cost-effective high-throughput sequencing necessary to accomplish full genome sequencing is by using Nanopore technology, which is a patented technology held by Harvard University and Oxford Nanopore Technologies and licensed to biotechnology companies.[14] To facilitate their full genome sequencing initiatives, Illumina licensed nanopore sequencing technology from Oxford Nanopore Technologies and Sequenom licensed the technology from Harvard University.[15][16] Another possible way to accomplish cost-effective high-throughput sequencing is by utilizing fluorophore technology. Pacific Biosciences is currently using this approach in their SMRT (single molecule real time) DNA sequencing technology.[17] Complete Genomics is developing DNA Nanoball (DNB) technology that are arranged on self-assembling arrays.[18] Pyrosequencing is a method of DNA sequencing based on the sequencing by synthesis principle.[19] The technique was developed by Pål Nyrén and his student Mostafa Ronaghi at the Royal Institute of Technology in Stockholm in 1996,[20][21][22] and is currently being used by 454 Life Sciences in their effort to deliver an affordable, fast and highly accurate full genome sequencing platform.[23]

Older techniques

Full genome sequencing of the entire human genome was first accomplished in 2000 partly through the use of shotgun sequencing technology. While full genome shotgun sequencing for small (4000–7000 base pair) genomes was already in use in 1979,[24] broader application benefited from pairwise end sequencing, known colloquially as double-barrel shotgun sequencing. As sequencing projects began to take on longer and more complicated genomes, multiple groups began to realize that useful information could be obtained by sequencing both ends of a fragment of DNA. Although sequencing both ends of the same fragment and keeping track of the paired data was more cumbersome than sequencing a single end of two distinct fragments, the knowledge that the two sequences were oriented in opposite directions and were about the length of a fragment apart from each other was valuable in reconstructing the sequence of the original target fragment.

The first published description of the use of paired ends was in 1990 as part of the sequencing of the human HPRT locus,[25] although the use of paired ends was limited to closing gaps after the application of a traditional shotgun sequencing approach. The first theoretical description of a pure pairwise end sequencing strategy, assuming fragments of constant length, was in 1991.[26] In 1995 Roach et al.introduced the innovation of using fragments of varying sizes,[27] and demonstrated that a pure pairwise end-sequencing strategy would be possible on large targets. The strategy was subsequently adopted by The Institute for Genomic Research (TIGR) to sequence the entire genome of the bacterium Haemophilus influenzae in 1995,[28] and then by Celera Genomics to sequence the entire fruit fly genome in 2000,[29] and subsequently the entire human genome. Applied Biosystems, now called Life Technologies, manufactured the shotgun sequencers utilized by both Celera Genomics and The Human Genome Project.

While shotgun sequencing was one of the first approaches utilized to successfully sequence the full genome of a human, it is too expensive and requires too long of a turn-around-time to be utilized for commercial purposes. Because of this, shotgun sequencing technology, even though it is still relatively 'new', is being displaced by technologies like pyrosequencing, SMRT sequencing, and nanopore technology.[30]

Race to commercialization

In October 2006, the X Prize Foundation, working in collaboration with the J. Craig Venter Science Foundation, established the Archon X Prize for Genomics,[31] intending to award US$10 million to "the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome."[32] However, higher accuracy rates (or confirmatory methods) are desirable for some clinical applications. An error rate of 1 in 100,000 bases, out of a total of six billion bases in the human diploid genome, would mean about 60,000 errors per genome, which is a significant number of false positives and negatives. For the latter it is not known where the errors occur . The error rates required for widespread clinical use, such as Predictive Medicine[33] is currently set by over 1400 clinical single gene sequencing tests [34] (for example, errors in BRCA1 gene for breast cancer risk analysis). As of June 2009, the Archon X Prize for Genomics remains unclaimed.

In 2007, Applied Biosystems started selling a new type of sequencer called SOLiD System, with the first sale to Helicos Biosciences in 2008.[35] Helicos stated that, utilizing the new sequencers, they will attempt to provide a full genome sequencing service with a target price of $72,000 per sample.[36] However, this price point is still too high some applications, and is only competitive to DNA arrays (at $500 per sample) in cases where more than 0.1% of the genome is desired.

In 2008 and 2009, both public and private companies have emerged that are now in a competitive race to be the first mover to provide a full genome sequencing platform that is commercially robust for both research and clinical use,[37] including Illumina,[38] Sequenom,[39] 454 Life Sciences,[40] Pacific Biosciences,[41] Complete Genomics,[42] Intelligent Bio-Systems,[43] Genome Corp.,[44] and Helicos BioScience[45]. These companies are heavily financed and backed by venture capitalists, hedge funds, investment banks and, in the case of Illumina, Sequenom and 454, heavy re-investment of revenue into research and development, mergers and acquisitions, and licensing initiatives.[46][47][48]

In the race to commercialize full genome sequencing, companies have made claims about being able to offer a service at a specific time for a specific price that have turned out to not be true. Intelligent Bio-Systems stated in November 2007 that by the end of 2008 they would release a platform capable of a providing a $5,000 full genome sequence, but, as of March 2009, no such platform has yet to be released.[49]

Pacific Biosciences stated that they will start selling their full genome sequencers in early 2010. While they didn't disclose the cost to sequence a single genome, they did state they may not release their second-generation machine capable of a $1,000 genome until 2013.[36] Complete Genomics, however, stated that they'll be able to provide a $5,000 full genome sequencing service by the summer of 2009.[50] The accuracy, precision, and reproducibility of both Pacific Biosciences and Complete Genomics technology, however, is still unknown.

A personal genomics company located in Massachusetts, Knome.com, currently provides genome sequencing services but the cost is about $99,500 per genome (down from $350,000 per genome initially),[51] the turn-around time is unknown, the accuracy is unknown, and the number of people was limited to 20 for the first year, and is still considered early stage commercialization of full genome sequencing, focusing on wealthy customers.[52]

As of January 2009, there are no indications that any of these companies have been hindered by the global recession. And thus, the race appears to be proceeding forward at full speed. [53]

At the end of February 2009, Complete Genomics released a full sequence of a human genome that was sequenced using their service. The data indicates that Complete Genomics' full genome sequencing service accuracy is just under 99.99%, meaning that there is an error in one out of every ten thousand base pairs. This means that their full sequence of the human genome will contain approximately 80,000-100,000 false positive errors in each genome. However, this accuracy rate was based on Complete Genomics' sequence that was completed utilizing a 90x depth of coverage (each base in the genome was sequenced 90 times) while their commercialized sequence is reported to be only 40x, so the accuracy may be substantially lower unless they can find some way to improve it before their first service release planned for the summer 2009. This accuracy rate may be acceptable for research purposes, and clinical use would require confirmation by other methods of any reportable alleles.[54][55] In March 2009, it was announced that Complete Genomics has signed a deal with the Broad Institute to sequence cancer patient's genomes and will be sequencing five full genomes to start.[56] In April 2009, Complete Genomics announced that it plans to sequence 1,000 full genome's between June 2009 and the end of the year and that they plan to be able to sequence one million full genomes per year by 2013.[57] Complete Genomics plans to officially launch in June 2009, although it is unknown if their lab will have received CLIA-certification by that time.

In June 2009, Illumina announced that they were launching their own Personal Full Genome Sequencing Service at a depth of 30X for $48,000 per genome.[58] This is still expensive for widespread consumer use, but the price may decrease substantially over the next few years as they realize economies of scale and given the competition with other companies such as Complete Genomics.[59][60] Jay Flatley, Illumina's President & CEO, stated that "during the next five years, perhaps markedly sooner," the price point for full genome sequencing will fall from $48,000 to under $1,000.[61] Illumina has already signed agreements to supply full genome sequencing services to multiple direct-to-consumer personal genomics companies.

Disruptive technology

Full genome sequencing provides information on a genome that is orders of magnitude larger than that provided by the current leader in sequencing technology, DNA arrays. For humans, DNA arrays currently provides genotypic information on up to one million genetic variants,[62][63][64] while full genome sequencing will provide information on all six billion bases in the human genome, or 3,000 times more data. Because of this, full genome sequencing is considered disruptive to the DNA array markets as the accuracy of both range from 99.98% to 99.999% (in non-repetitive DNA regions) and their cost of $5000 per 6 billion base pairs is competitive (for some applications) with DNA arrays ($500 per 1 million basepairs).[40] Agilent, another established DNA array manufacturer, is working on targeted (selective region) genome sequencing technologies[65]. It is thought that Affymetrix, the pioneer of array technology in the 1990s, has fallen behind due to significant corporate and stock turbulence and is currently not working on any known full genome sequencing approach.[66][67][68] It is unknown what will happen to the DNA array market once full genome sequencing becomes commercially widespread, especially as companies and laboratories providing this disruptive technology start to realize economies of scale. It is postulated, however, that this new technology may significantly diminish the total market size for arrays and any other sequencing technology once it becomes commonplace for individuals and newborns to have their full genomes sequenced.[69]

Societal impact

Inexpensive, time-efficient full genome sequencing will be a major accomplishment not only for the field of Genomics, but for the entire human civilization because, for the first time, individuals will be able to have their entire genome sequenced. Utilizing this information, it is speculated that health care professionals, such as physicians and genetic counselors, will eventually be able to use genomic information to predict what diseases a person may get in the future and attempt to either minimize the impact of that disease or avoid it altogether through the implementation of personalized, preventive medicine. Full genome sequencing will allow health care professionals to analyze the entire human genome of an individual and therefore detect all disease-related genetic variants, regardless of the genetic variant's prevalence or frequency. This will enable the rapidly emerging medical fields of Predictive Medicine and Personalized Medicine and will mark a significant leap forward for the clinical genetic revolution. Full genome sequencing is clearly of great importance for research into the basis of genetic disease. However, it should be recognized that despite advancements in genome sequencing technology, incomplete understanding of the significance of individual variants or combinations of variants will limit the widespread usefulness of full genome sequencing in medicine until its clinical utility can be demonstrated.

Illumina's CEO, Jay Flatley, stated in February 2009 that "A complete DNA read-out for every newborn will be technically feasible and affordable in less than five years, promising a revolution in healthcare" and that "by 2019 it will have become routine to map infants' genes when they are born."[70] However, this potential use of genome sequencing runs counter to established norms for genetic testing of asymptomatic minors that have been well established in the field of genetic counseling.[71][72][73][74]